Package org.biojava.bio.program.ssaha

Interface DataStoreFactory

All Known Implementing Classes:

CompactedDataStoreFactory, MappedDataStoreFactory, NIODataStoreFactory

public interface DataStoreFactory

Builder for a data store.

Author:

Matthew Pocock

Method Summary

Modifier and Type	Method	Description
DataStore	buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)	Build a new DataStore.
DataStore	getDataStore(java.io.File storeFile)	Get a pre-built data store associated with a file.

Method Detail

getDataStore

DataStore getDataStore(java.io.File storeFile)
                throws java.io.IOException

Get a pre-built data store associated with a file.

Parameters:

storeFile - the File to map in as a data store

Returns:

the DataStore made by mapping the file

Throws:

java.io.IOException - if the file could not be mapped

buildDataStore

DataStore buildDataStore(java.io.File storeFile,
                         SequenceDB seqDB,
                         Packing packing,
                         int wordLength,
                         int threshold)
                  throws IllegalAlphabetException,
                         java.io.IOException,
                         BioException

Build a new DataStore.

Parameters:

storeFile - the file to store the data store

seqDB - the SequenceDB to store in the data store

packing - the Packing used to bit-encode the sequences

wordLength - the number of symbols per word

threshold - the number of times a word must appear to be ignored

Throws:

IllegalAlphabetException - if the packing does not agree with the sequences

BioException - if there is a problem building the data store

java.io.IOException